RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2507
(111 letters)
>gnl|CDD|217380 pfam03133, TTL, Tubulin-tyrosine ligase family. Tubulins and
microtubules are subjected to several post-translational
modifications of which the reversible
detyrosination/tyrosination of the carboxy-terminal end
of most alpha-tubulins has been extensively analysed.
This modification cycle involves a specific
carboxypeptidase and the activity of the
tubulin-tyrosine ligase (TTL). The true physiological
function of TTL has so far not been established.
Tubulin-tyrosine ligase (TTL) catalyzes the
ATP-dependent post-translational addition of a tyrosine
to the carboxy terminal end of detyrosinated
alpha-tubulin. In normally cycling cells, the
tyrosinated form of tubulin predominates. However, in
breast cancer cells, the detyrosinated form frequently
predominates, with a correlation to tumour
aggressiveness. On the other hand, 3-nitrotyrosine has
been shown to be incorporated, by TTL, into the carboxy
terminal end of detyrosinated alpha-tubulin. This
reaction is not reversible by the carboxypeptidase
enzyme. Cells cultured in 3-nitrotyrosine rich medium
showed evidence of altered microtubule structure and
function, including altered cell morphology, epithelial
barrier dysfunction, and apoptosis. Bacterial homologs
of TTL are predicted to form peptide tags. Some of these
are fused to a 2-oxoglutarate Fe(II)-dependent
dioxygenase domain.
Length = 291
Score = 78.1 bits (193), Expect = 1e-18
Identities = 31/52 (59%), Positives = 36/52 (69%)
Query: 6 YELYGFDILIDSDLKPWLLEVNLSPSLGCDTPLDTRLKSAMLADTLTLVGIP 57
+ELYGFD +ID +LKPWLLEVN SPSL T LD RLK ++ D L V P
Sbjct: 234 FELYGFDFMIDENLKPWLLEVNASPSLHSTTKLDARLKEQLIDDVLNSVVPP 285
>gnl|CDD|222735 pfam14398, ATPgrasp_YheCD, YheC/D like ATP-grasp. A member of the
ATP-grasp fold predicted to be involved in the
modification/biosynthesis of spore-wall and capsular
proteins.
Length = 262
Score = 34.2 bits (79), Expect = 0.006
Identities = 12/25 (48%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 7 ELYGFDILIDSDLKPWLLEVNLSPS 31
EL G DI +D+ + WLLE N P
Sbjct: 211 EL-GIDIGLDTQGRIWLLEANSKPG 234
>gnl|CDD|234948 PRK01372, ddl, D-alanine--D-alanine ligase; Reviewed.
Length = 304
Score = 31.2 bits (72), Expect = 0.064
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 12 DILIDSDLKPWLLEVNLSP 30
D ++D D KP+LLEVN P
Sbjct: 252 DFMLDEDGKPYLLEVNTQP 270
>gnl|CDD|202916 pfam04174, CP_ATPgrasp_1, A circularly permuted ATPgrasp. An
ATP-grasp family that is present both as catalytically
active and inactive versions. Contextual analysis
suggests that it functions in a distinct peptide
synthesis/modification system that additionally
contains a transglutaminase, an NTN-hydrolase, the
Alpha-E domain, and a transglutaminase fused N-terminal
to a circularly permuted COOH-NH2 ligase. The inactive
forms are often fused N-terminal to the Alpha-E domain.
Length = 331
Score = 31.1 bits (71), Expect = 0.076
Identities = 9/25 (36%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 8 LYGFDILIDSDLKPWLLEVNL-SPS 31
+YG D++ D + +LE N +PS
Sbjct: 70 VYGADLVRGPDGRWRVLEDNTRAPS 94
>gnl|CDD|185368 PRK15471, PRK15471, chain length determinant protein WzzB;
Provisional.
Length = 325
Score = 29.3 bits (66), Expect = 0.30
Identities = 15/42 (35%), Positives = 28/42 (66%), Gaps = 2/42 (4%)
Query: 49 DTLTLVGIPALDPMLRHNSTKRSPFLSSSHTLRTKCSLGDMD 90
DTL L+G AL+ M++H +T+ P + S + +T+ +L D++
Sbjct: 226 DTLFLLGSEALESMIKHEATR--PLVFSPNYYQTRQNLLDIE 265
>gnl|CDD|233813 TIGR02291, rimK_rel_E_lig, alpha-L-glutamate ligase-related
protein. Members of this protein family contain a
region of homology to the RimK family of
alpha-L-glutamate ligases (TIGR00768), various members
of which modify the Glu-Glu C-terminus of ribosomal
protein S6, or tetrahydromethanopterin, or a form of
coenzyme F420 derivative. Members of this family are
found so far in various Vibrio and Pseudomonas species
and some other gamma and beta Proteobacteria. The
function is unknown.
Length = 317
Score = 27.5 bits (61), Expect = 1.3
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 5/35 (14%)
Query: 3 SEKYELYGF-----DILIDSDLKPWLLEVNLSPSL 32
+ +EL G D+++D + P +LE+N P L
Sbjct: 238 ASCWELTGLGYMGVDMVLDKEEGPLVLELNARPGL 272
>gnl|CDD|234489 TIGR04172, DGQHR_dnd_1, DNA phosphorothioation-associated DGQHR
protein 1. The DND system produces an
phosphorothioation modification to DNA, replacing a
non-bridging oxygen of a phosphate group with sulfur.
The modification causes DNA degradation during
electrophoresis in Tris buffer. This protein, like DndB
(TIGR03233), contains a DGQHR domain (TIGR03187), which
also occurs in several contexts that suggest lateral
transfer rather than DNA phosphorothioation-dependent
restriction.
Length = 380
Score = 27.8 bits (62), Expect = 1.3
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 6/53 (11%)
Query: 3 SEKYELYGFDILIDSDLKPW---LLEVNLSPSLG--CDTPLDTRLKSAMLADT 50
S YEL+G+D + + + W L V L+ L ++PL ++K A +D+
Sbjct: 166 SLAYELFGYD-VDEEPREYWSPEKLAVYLTRKLNTDSESPLYQKIKLAAKSDS 217
>gnl|CDD|235109 PRK03187, tgl, transglutaminase; Provisional.
Length = 272
Score = 27.3 bits (61), Expect = 1.6
Identities = 10/48 (20%), Positives = 17/48 (35%), Gaps = 4/48 (8%)
Query: 43 KSAMLADTLTLVGIPALDPMLRHNSTKRSPFLSSSHTLRTKCSLGDMD 90
+SA L D +T + L R S + S + ++G
Sbjct: 226 QSAYLTDQITRLDSRYLSQFARPFSPQTSIGRDDAIV----ATVGSTT 269
>gnl|CDD|169002 PRK07546, PRK07546, hypothetical protein; Provisional.
Length = 209
Score = 26.5 bits (59), Expect = 2.5
Identities = 15/49 (30%), Positives = 21/49 (42%), Gaps = 19/49 (38%)
Query: 30 PSLGCDTPL-----DTRLKSAMLADTLTLVGIPALDPMLRHNSTKRSPF 73
P L DT TRL SA DP+LR+ +T+R+ +
Sbjct: 79 PPLPPDTVWRVAIARTRLDSA--------------DPLLRYKTTRRAAY 113
>gnl|CDD|239890 cd04443, DEP_GPR155, DEP (Dishevelled, Egl-10, and Pleckstrin)
domain found in GPR155-like proteins. GRP155-like
proteins, also known as PGR22, contain an N-terminal
permease domain, a central transmembrane region and a
C-terminal DEP domain. They are orphan receptors of the
class B G protein-coupled receptors. Their function is
unknown.
Length = 83
Score = 25.4 bits (56), Expect = 3.8
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 17 SDLKPWLLEVNLSP 30
DL WL+EV L+
Sbjct: 34 CDLVSWLIEVGLAQ 47
>gnl|CDD|225198 COG2316, COG2316, Predicted hydrolase (HD superfamily) [General
function prediction only].
Length = 212
Score = 26.0 bits (57), Expect = 4.8
Identities = 17/50 (34%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 4 EKYELYGFDILIDSDLKPWLLEVNLSPSLGCDTPLDTRLKSAMLA-DTLT 52
E++ L+G +IL + D+ +L+ + + TP +TRL+ A+ A D LT
Sbjct: 92 EEHGLWGVEILREEDVSEEILDAIMGHAAYTGTPRETRLEQALFAVDELT 141
>gnl|CDD|177351 PHA02117, PHA02117, glutathionylspermidine synthase
domain-containing protein.
Length = 397
Score = 26.0 bits (57), Expect = 4.9
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 7/31 (22%)
Query: 8 LYG-FDILIDSDLKPWLLEVNLSPSLGCDTP 37
LYG FD+++ + P +LE N DTP
Sbjct: 107 LYGRFDLIMTPNGGPKMLEYN------ADTP 131
>gnl|CDD|112559 pfam03749, SfsA, Sugar fermentation stimulation protein. This
family contains Sugar fermentation stimulation proteins.
Which is probably a regulatory factor involved in
maltose metabolism. SfsA has been shown to bind DNA and
it contains a helix-turn-helix motif that probably binds
DNA at its C-terminus.
Length = 215
Score = 25.8 bits (57), Expect = 5.7
Identities = 6/22 (27%), Positives = 8/22 (36%)
Query: 5 KYELYGFDILIDSDLKPWLLEV 26
KY D L+ +EV
Sbjct: 99 KYGNSRIDFLLKEPEGRCYVEV 120
>gnl|CDD|233310 TIGR01205, D_ala_D_alaTIGR, D-alanine--D-alanine ligase. This
model describes D-Ala--D-Ala ligase, an enzyme that
makes a required precursor of the bacterial cell wall.
It also describes some closely related proteins
responsible for resistance to glycopeptide antibiotics
such as vancomycin. The mechanism of glyopeptide
antibiotic resistance involves the production of
D-alanine-D-lactate (VanA and VanB families) or
D-alanine-D-serine (VanC). The seed alignment contains
only chromosomally encoded D-ala--D-ala ligases, but a
number of antibiotic resistance proteins score above the
trusted cutoff of this model [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan].
Length = 315
Score = 25.3 bits (56), Expect = 7.8
Identities = 6/19 (31%), Positives = 11/19 (57%)
Query: 12 DILIDSDLKPWLLEVNLSP 30
D +D + + +L E+N P
Sbjct: 267 DFFLDEEGEIYLNEINTIP 285
>gnl|CDD|224102 COG1181, DdlA, D-alanine-D-alanine ligase and related ATP-grasp
enzymes [Cell envelope biogenesis, outer membrane].
Length = 317
Score = 25.3 bits (56), Expect = 8.3
Identities = 9/22 (40%), Positives = 12/22 (54%), Gaps = 1/22 (4%)
Query: 10 GFDILIDSDL-KPWLLEVNLSP 30
D +D D + LLEVN +P
Sbjct: 265 RVDFFVDDDEGEFVLLEVNTNP 286
>gnl|CDD|176556 cd08619, PI-PLCXDc_plant, Catalytic domain of
phosphatidylinositol-specific phospholipase C, X domain
containing proteins found in plants. The CD corresponds
to the catalytic domain present in uncharacterized plant
phosphatidylinositol-specific phospholipase C, X domain
containing proteins (PI-PLCXD). The typical eukaryotic
phosphoinositide-specific phospholipase C (PI-PLC, EC
3.1.4.11) has a multidomain organization that consists
of a PLC catalytic core domain, and various regulatory
domains. The catalytic core domain is assembled from two
highly conserved X- and Y-regions split by a divergent
linker sequence. In contrast, plant PI-PLCXDs contain a
single TIM-barrel type catalytic domain, X domain, and
are more closely related to bacterial PI-PLCs, which
participate in Ca2+-independent PI metabolism,
hydrolyzing the membrane lipid phosphatidylinositol (PI)
to produce phosphorylated myo-inositol and
diacylglycerol (DAG). Although the biological function
of plant PI-PLCXDs still remains unclear, it may
distinct from that of typical eukaryotic PI-PLCs.
Length = 285
Score = 25.2 bits (55), Expect = 9.0
Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 3/64 (4%)
Query: 7 ELYGFDILIDSDLKPWLLEVNLSPSLGCDTPLDTRLKSAMLADTLTLVGIPALDPMLRHN 66
Y D ID+DL E N+ +L P D+R + +T+T +
Sbjct: 181 SAYLKDNWIDTDLPVTKFESNIK-NLLEQPPQDSRKYFYRVENTVT--PQFDNPILCVKP 237
Query: 67 STKR 70
T+R
Sbjct: 238 VTRR 241
>gnl|CDD|225190 COG2308, COG2308, Uncharacterized conserved protein [Function
unknown].
Length = 488
Score = 25.0 bits (55), Expect = 9.7
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 9 YGFDILIDSDLKPWLLEVNL-SPS 31
G D++ D D +LE NL +PS
Sbjct: 148 CGTDLIRDPDGNFQVLEDNLRAPS 171
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.134 0.395
Gapped
Lambda K H
0.267 0.0741 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,391,439
Number of extensions: 435221
Number of successful extensions: 294
Number of sequences better than 10.0: 1
Number of HSP's gapped: 294
Number of HSP's successfully gapped: 21
Length of query: 111
Length of database: 10,937,602
Length adjustment: 75
Effective length of query: 36
Effective length of database: 7,611,052
Effective search space: 273997872
Effective search space used: 273997872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.2 bits)